Nuclear export of the HIV genome: A Molecular Dynamics Study of the Interactions and Structure of HIV Rev and Host CRM1 during Export Summary The HIV virus is a pandemic lentivirus which has no existing cure or vaccine. Current treatments consist of powerful drug cocktails containing multiple drugs targeting multiple aspects of the viral lifecycle. Besides the toxic side effects caused by many of these drugs, in the majority of cases the virus develops resistance to the drugs used, forcing a switch to more toxic and less effective drugs, culminating in the escape of the virus from drug control. Despite the variety of drugs available, no current drugs target a critical part of the viral lifecycle, the Rev and Exportin-1 (Crm1) mediated export of the full viral genome during active viral replication. Here, the viral protein Rev forms a six-part oligomer on the Rev Response Element (RRE) of the viral genome. This oligomer then recruits copies of the host protein crm1 to export the genome out of the cell nucleus, bypassing the standard pathways of mRNA splicing and export. Attempts to target this export pathway are limited by a combination of poor structural and mechanistic understandings of the proteins involved. While experimental methods have been successful in elucidating broad details of the process, the binding regions of the proteins and RNA involved, and even some details of structure and mechanism, the understanding derived so far is incomplete and uncertain, inadequate for use in truly in-depth studies or to support attempts to modify the pathway. Utilizing the fine spatiotemporal resolution of computational and molecular dynamics approaches, these problems can be overcome. In this project, these methods will be used to investigate the entire process of export complex formation, from the attachment of the first Rev monomer to the RRE all the way up the recruitment of multiple crm1 copies, and will use them to address outstanding questions in the field and to open the way for further investigation. Specifically, this study will validate previous proposed mechanisms and structures, deeply investigate the mechanism of Rev oligomer-RRE assembly, including the importance of cooperativity, and provide a complete structure of this assembly. In addition, binding of the assembly with crm1 will be investigated, and the results used to address such topics as the maximal plausible number of bound crm1 proteins and the importance of all six Rev copies in binding. Finally, and most importantly, a structure of the entire export complex will be generated, which can be used in future mechanistic and computational studies, or as a guidepost for future experimental studies. In the long-run it may even be possible to put these results to practical use. PUBLIC HEALTH RELEVANCE: Nuclear export of the HIV genome: A Molecular Dynamics Study of the Interactions and Structure of HIV Rev and Host CRM1 during Export Narrative Despite extensive research, the process by which HIV Rev oligomerizes on the Rev Response Element (RRE) sequence of the viral genome and recruits crm1 to export this genome is not well-characterized. Many of the obstacles to experimental studies that frustrate attempts to fully understand the process fall away when computational methods are considered instead. The greater understanding of the Rev export pathway that will be obtained when such methods are used will prove invaluable to the field of study, and may provide intriguing avenues of exploration into one of the few steps of HIV replication which is not yet the target of therapy.